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https://www.mdanderson.org/research/departments-labs-institutes/programs-centers/michale-e-keeling-center-for-comparative-medicine-and-research/national-center-for-chimpanzee-care.html

One of only four NCRR-supported centers with the capability to conduct biomedical research in the chimpanzee, it offers chimpanzee-derived cell lines, antibodies and other biological materials, along with a registry of biologic reagents that are known to work in the chimpanzee. The Resource and Management Core is responsible for providing animal resources, tissues/biological fluids, cell lines, expert advice and research support to NIH extramural and intramural programs, other federal agencies and private sponsors. The Resource-Related Research Core conducts research to improve the health of the animals maintained, with special emphasis on studies that will enhance the usefulness of the chimpanzee as a model for studies of human disease. Resource-related research will focus on characterization of the immune system of the chimpanzee, expansion of our understanding of chimpanzee cardiomyopathy as a potential human disease model and comparisons of the physiologic and immunological consequences of research manipulations on chimpanzees trained to voluntarily cooperate with research procedures. By expanding the resources available, conducting resource-related research and containing costs, the CBRR will continue to provide a critically important, highly specialized research resource to address important human health issues.

Proper citation: Chimpanzee Biomedical Research Resource (RRID:SCR_006289) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Proper citation: oligo (RRID:SCR_015729) Copy   

•   Source: SciCrunch Registry

https://www.mristudio.org/

An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration

Proper citation: MRI Studio (RRID:SCR_001398) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/pneuma/

A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insulin regulation and free fatty acid (FFA) regulation. * Changes in sympathetic activity from the autonomic portion of PNEUMA produce changes in epinephrine output, which in turn affects the metabolic sub-model. * Inputs from the dietary intake of glucose and external interventions, such as insulin injections, have also been incorporated. * Also incorporated is autonomic feedback from the metabolic component to the rest of PNEUMA: changes in insulin level lead to changes in sympathetic tone. System Requirements: PNEUMA requires Matlab R2007b or higher with the accompanying version of Simulink to be installed on your computer.

Proper citation: PNEUMA (RRID:SCR_001391) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/downloads/montage_rts2000.shtm

Software program for creating montages from multiphoton microscopy.

Proper citation: Montage RTS2000 (RRID:SCR_013439) Copy   

•   Source: SciCrunch Registry

http://ligand-expo.rutgers.edu/

An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.

Proper citation: Ligand Expo (RRID:SCR_006636) Copy   

•   Source: SciCrunch Registry

http://www.pathbase.net/

Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)

Proper citation: Pathbase (RRID:SCR_006141) Copy   

•   Source: SciCrunch Registry

https://neuroscienceblueprint.nih.gov/Resources-Tools/Blueprint-Resources-Tools-Library

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups.

Proper citation: Biomedical Informatics Research Network (RRID:SCR_005163) Copy   

•   Source: SciCrunch Registry

http://zebrafish.org

Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.

Proper citation: Zebrafish International Resource Center (RRID:SCR_005065) Copy   

•   Source: SciCrunch Registry

https://www.aplysia.earth.miami.edu/

Center where Aplysia californica are cultured and raised for research purposes. Aplysia from the facility serve in research on genomics, human brain function, toxicology for developmental studies, natural products, chemistry for isolation of novel anti-tumor and antibacterial compounds, in the study of transport by digestive tissues and have potential for use in studies of substance addiction and nerve senescence and regeneration.

Proper citation: National Resource for Aplysia (RRID:SCR_008361) Copy   

•   Source: SciCrunch Registry

http://ultrascan.aucsolutions.com/

Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.

Proper citation: UltraScan (RRID:SCR_018126) Copy   

•   Source: SciCrunch Registry

https://dice-database.org

Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

https://github.com/macmanes-lab/BinPacker/blob/master/README

Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

Proper citation: BinPacker (RRID:SCR_017038) Copy   

•   Source: SciCrunch Registry

http://bio3d.colorado.edu/SerialEM/

Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function.

Proper citation: SerialEM (RRID:SCR_017293) Copy   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Proper citation: ToppCluster (RRID:SCR_001503) Copy   

•   Source: SciCrunch Registry

https://omictools.com/dog-picker-tool

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software tool for general particle picking in the single-particle processing of unknown macromolecules. Reference free particle picker with ability to sort particles based on size or it can be used to bootstrap the creation of templates or training datasets for other particle pickers. Used to facilitate particle selection in single particle electron microscopy., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DoG picker (RRID:SCR_016655) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home

Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools.

Proper citation: Appion Package (RRID:SCR_016734) Copy   

•   Source: SciCrunch Registry

http://www.civm.duhs.duke.edu/neuro2012ratatlas/

Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.

Proper citation: Adult Wistar Rat Atlas (RRID:SCR_006288) Copy   

•   Source: SciCrunch Registry

http://www.oasis-brains.org/

Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.

Proper citation: Open Access Series of Imaging Studies (RRID:SCR_007385) Copy   

•   Source: SciCrunch Registry